[Bioc-devel] arrow dependent packages fail to build on macOS

[Hervé Pagès]

Hi Edward,

arrow is a CRAN package with Mac binaries available for R 4.4 so our 
build system just install that. Note that Mac package binaries should be 
self-contained (they use static linking), so they should **never** 
require any external system library.

Not sure why we see this error on lconway. It could be that there was a 
problem with the Mac binary provided by CRAN (it looks like they updated 
the binary on Sept 12), or something went wrong when it landed on 
lconway, hard to know. In any case, I just reinstalled the package on 
lconway and that seems to have solved the problem, that is, now I can 
library(arrow) in an interactive session on the machine.

I might have done this too late for the fix to have any impact on 
tomorrow's build report for 3.20. Let's see how things are going for 
BayesSpace on Friday's report.

Best,

H.

On 10/23/24 01:29, Edward Zhao wrote:
> Hello,
>
> I have made updates to my package BayesSpace on the devel branch and it
> shows an error on macOS only due to an error with the arrow dependency:
>
> unable to load shared object
> '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so':
> dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so,
> 0x0006): symbol not found in flat namespace (_ZSTD_compress)
>
>
> This is a CRAN package that passes CRAN checks
> <https://cran.r-project.org/web/checks/check_results_arrow.html>, but it
> seems like they are having problems on macOS (
> https://github.com/apache/arrow/issues/44206,
> https://github.com/apache/arrow/issues/40667), which is the version on the
> build environment. There is a comment here that suggests installing from
> r-universe instead of CRAN.
>
> I've been messaging with Martin Grigorov on slack, who suggested that I
> should request zstd to be installed on the builder machine. My collaborator
> Senbai (cc'd) who has been looking into this also suggested to install
> libarrow with "full features" since the current libarrow on the machine
> does not support zstd compression type.
>
> Please let me know if there's anything I can do to help get this resolved.
> It is affecting not only my package but also others that use arrow (e.g.
> VisiumIO<https://bioconductor.org/checkResults/devel/bioc-LATEST/VisiumIO/>,
> SpatialFeatureExperiment
> <https://bioconductor.org/checkResults/devel/bioc-LATEST/SpatialFeatureExperiment/>).
> Thanks!
>
> Best,
> Edward
>
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>
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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